The uncontrolled natural pre-fermentation process of coconut water represents great hidden safety hazards, unstable production, and impact on the quality of nata de coco–the trade name of bacterial cellulose (BC) in food industry. In this study, BC production from Komagataeibacter nataicola Q2 was conducted in the media of coconut water (50%, v/v) pre-fermented by 11 coconut-sourced yeast strains in static. Results suggested that coconut water pre-fermented by different yeast strains had varied effects on the production of BC. Compared with the use of fresh coconut water, the use of coconut water pre-fermented by Saccharomyces cerevisiae SC7 increased the BC yield by 165%. Both natural pre-fermentation and SC7 pre-fermentation altered the concentrations of amino acids in fresh coconut water. The addition of selected amino acids aspartic acid, glutamic acid, serine, methionine, threonine, isoleucine, phenylalanine, and proline at different concentrations had varied effects on the production of BC. The yield of BC was the highest when adding 3.0% (w/v) methionine. Moreover, adding 3.0% methionine allowed the production of BC with larger loops of looser aggregated microfibers, increased the crystallinity of BC from 64.8% to 69.4%, but decreased the temperature of maximum weight loss rate, hardness, and adhesiveness from 223 °C, 8.68 kg, and 92.8 g.sec to 212 °C, 7.01 kg, and 58.5 g.sec, respectively, in the test condition.